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- PDB-3n90: The 1.7 Angstrom resolution crystal structure of AT2G44920, a pen... -

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Basic information

Entry
Database: PDB / ID: 3n90
TitleThe 1.7 Angstrom resolution crystal structure of AT2G44920, a pentapeptide repeat protein from Arabidopsis thaliana thylakoid lumen.
ComponentsThylakoid lumenal 15 kDa protein 1, chloroplastic
KeywordsUNKNOWN FUNCTION / right-handed quadrilateral beta helix / pentapeptide repeat protein / repeated-five residue fold / chloroplast lumen
Function / homology
Function and homology information


thylakoid lumen / chloroplast thylakoid / thylakoid / chloroplast thylakoid lumen / chloroplast thylakoid membrane / chloroplast / cytosol
Similarity search - Function
Thylakoid lumenal 15kDa protein 1-like / Pentapeptide repeats (8 copies) / Pentapeptide repeat / E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Thylakoid lumenal 15 kDa protein 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsNi, S. / Mckgookey, M. / Tinch, S.L. / Jones, A.N. / Jayaraman, S. / Kennedy, M.A.
CitationJournal: To be Published
Title: The 1.7 Angstrom resolution crystal structure of AT2G44920, a pentapeptide repeat protein from Arabidopsis thaliana thylakoid lumen.
Authors: Ni, S. / Mckgookey, M. / Tinch, S.L. / Jones, A.N. / Jayaraman, S. / Kennedy, M.A.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thylakoid lumenal 15 kDa protein 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3482
Polymers16,2521
Non-polymers961
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.064, 75.444, 59.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thylakoid lumenal 15 kDa protein 1, chloroplastic / p15


Mass: 16251.973 Da / Num. of mol.: 1 / Fragment: UNP residues 81-224 / Mutation: V173M, T174M
Source method: isolated from a genetically manipulated source
Details: T7 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g44920, T13E15.7 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O22160
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: well buffer: 2.5M ammonium sulfate, 0.5M sodium acetate; Sample buffer: 0.25M sodium chloride, 10% glycerol, 0.02M Tris, pH 7.8 protein concentration=15mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2009
Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 14963 / Num. obs: 14963 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Redundancy: 1.87 % / Biso Wilson estimate: 19.93 Å2 / Rsym value: 0.081 / Net I/σ(I): 40.84
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 1.92 % / Mean I/σ(I) obs: 18.9 / Num. unique all: 2143 / Rsym value: 0.066 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.662 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25851 748 5 %RANDOM
Rwork0.22631 ---
obs0.2279 14963 99.2 %-
all-14963 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 5 103 1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221089
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9621469
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2652550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92615179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.876157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2536
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2745
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.5716
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54821118
X-RAY DIFFRACTIONr_scbond_it2.633397
X-RAY DIFFRACTIONr_scangle_it4.0684.5351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 1053 -
Rwork0.275 1053 -
obs--99.91 %

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